A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT (Q30481618)

14 August 2017

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT (English)

1 reference

14 August 2017

Jie Hu

1

1 reference

14 August 2017

Ao Ma

series ordinal

2

1 reference

14 August 2017

Aaron R Dinner

series ordinal

3

1 reference

14 August 2017

language of work or name

English

0 references

publication date

19 March 2008

1 reference

Proceedings of the National Academy of Sciences of the United States of America

14 August 2017

6

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based on heuristic

inferred from page(s)

published in

1 reference

14 August 2017

105

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14 August 2017

12

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14 August 2017

4615-4620

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Enzymatic capture of an extrahelical thymine in the search for uracil in DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Activation mechanism of a signaling protein at atomic resolution from advanced computations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Reaction coordinate of an enzymatic reaction revealed by transition path sampling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Interactions of human O6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Directed evolution of O6-alkylguanine-DNA alkyltransferase for applications in protein labeling.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Computational approaches for investigating base flipping in oligonucleotides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Targeted modulation of MGMT: clinical implications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Dynamic opening of DNA during the enzymatic search for a damaged base

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Transition-path sampling of β-hairpin folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

DNA-binding mechanism of O6-alkylguanine-DNA alkyltransferase. Effects of protein and DNA alkylation on complex stability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Crystal structure of the human O(6)-alkylguanine-DNA alkyltransferase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Investigation of the role of tyrosine-114 in the activity of human O6-alkylguanine-DNA alkyltranferase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Genetic neural networks for quantitative structure-activity relationships: improvements and application of benzodiazepine affinity for benzodiazepine/GABAA receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

HhaI methyltransferase flips its target base out of the DNA helix

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Automatic method for identifying reaction coordinates in complex systems.

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0708058105

DNA binding and nucleotide flipping by the human DNA repair protein AGT.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0708058105

The structure of the human AGT protein bound to DNA and its implications for damage detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0708058105

The origins of high-affinity enzyme binding to an extrahelical DNA base

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0708058105

A general method for the covalent labeling of fusion proteins with small molecules in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0708058105

Dynamic coupling between coordinates in a model for biomolecular isomerization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0708058105

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0708058105

Extensions to the likelihood maximization approach for finding reaction coordinates.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Obtaining reaction coordinates by likelihood maximization.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2290773

Push and pull of base flipping

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18353991

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Bias annealing: a method for obtaining transition paths de novo

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18353991

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0708058105

1 reference

14 August 2017

0 references

1 reference

14 August 2017

1 reference